Title: vcd Extensions and Additions
Description: Provides additional data sets, methods and documentation to complement the vcd package for Visualizing Categorical Data
and the gnm package for Generalized Nonlinear Models.
In particular, vcdExtra extends mosaic, assoc and sieve plots from vcd to handle glm() and gnm() models and
adds a 3D version in mosaic3d. Additionally, methods are provided for comparing and visualizing lists of
glm and loglm objects.
Author: Michael Friendly [aut, cre], Heather Turner [ctb], Achim Zeileis [ctb], Duncan Murdoch [ctb], David Firth [ctb]
Maintainer: Michael Friendly
Diff between vcdExtra versions 0.6-3 dated 2014-10-31 and 0.6-5 dated 2015-01-02
DESCRIPTION | 17 MD5 | 106 +-- NAMESPACE | 5 NEWS | 10 R/LRstats.R |only R/collapse.table.R | 5 R/vcdExtra-deprecated.R |only build/vignette.rds |binary data/Abortion.rda |binary data/Accident.RData |binary data/Alligator.RData |binary data/Bartlett.rda |binary data/Caesar.rda |binary data/Cancer.rda |binary data/Cormorants.RData |only data/CyclingDeaths.RData |binary data/DaytonSurvey.RData |binary data/Depends.RData |binary data/Detergent.rda |binary data/Donner.RData |binary data/Draft1970.RData |binary data/Draft1970table.RData |binary data/Dyke.rda |binary data/Fungicide.rda |binary data/GSS.rda |binary data/Geissler.RData |binary data/Gilby.rda |binary data/HairEyePlace.RData |binary data/Hauser79.RData |binary data/Heart.rda |binary data/Heckman.rda |binary data/Hoyt.rda |binary data/ICU.RData |binary data/JobSat.rda |binary data/Mammograms.RData |binary data/Mental.rda |binary data/Mobility.rda |binary data/PhdPubs.RData |binary data/ShakeWords.RData |binary data/TV.rda |binary data/Titanicp.rda |binary data/Toxaemia.RData |binary data/Vietnam.RData |binary data/Vietnam.rda |binary data/Vote1980.RData |binary data/Yamaguchi87.RData |binary inst/doc/vcd-tutorial.R | 1524 ++++++++++++++++++++++----------------------- inst/doc/vcd-tutorial.Rnw | 2 man/Cormorants.Rd |only man/HairEyePlace.Rd | 2 man/LRstats.Rd |only man/TV.Rd | 10 man/collapse.table.Rd | 8 man/cutfac.Rd | 39 - man/vcdExtra-deprecated.Rd |only man/vcdExtra-package.Rd | 4 vignettes/vcd-tutorial.Rnw | 2 57 files changed, 889 insertions(+), 845 deletions(-)
Title: Estimating birth and death rates based on phylogenies
Description: (i) For a given species phylogeny on present day data which is calibrated to calendar-time, a method for estimating maximum likelihood speciation and extinction processes is provided. The method allows for non-constant rates. Rates may change (1) as a function of time, i.e. rate shifts at specified times or mass extinction events (likelihood implemented as LikShifts, optimization as bd.shifts.optim and visualized as bd.shifts.plot) or (2) as a function of the number of species, i.e. density-dependence (likelihood implemented as LikDD and optimization as bd.densdep.optim) or (3) extinction rate may be a function of species age (likelihood implemented as LikAge and optimization as bd.age.optim.matlab). Note that the methods take into account the whole phylogeny, in particular it accounts for the "pull of the present" effect. (1-3) can take into account incomplete species sampling, as long as each species has the same probability of being sampled. For a given phylogeny on higher taxa (i.e. all but one species per taxa are missing), where the number of species is known within each higher taxa, speciation and extinction rates can be estimated under model (1) (implemented within LikShifts and bd.shifts.optim with groups !=0). (ii) For a given phylogeny with sequentially sampled tips, e.g. a virus phylogeny, rates can be estimated under a model where rates vary across time using bdsky.stt.optim based on likelihood LikShiftsSTT (extending LikShifts and bd.shifts.optim). Furthermore, rates may vary as a function of host types using LikTypesSTT (multitype branching process extending functions in R package diversitree). This function can furthermore calculate the likelihood under an epidemiological model where infected individuals are first exposed and then infectious.
Author: Tanja Stadler
Maintainer: Tanja Stadler
Diff between TreePar versions 3.2 dated 2014-11-08 and 3.3 dated 2015-01-02
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- man/LikAge.Rd | 37 ++++++++++++++++++------------------- man/LikShifts.Rd | 9 ++++++--- man/TreePar-package.Rd | 4 ++-- man/bd.age.optim.matlab.Rd | 41 ++++++++++++++++++++--------------------- man/bd.densdep.optim.Rd | 6 ++++-- man/create.mat.Rd | 20 ++++++++++---------- 8 files changed, 71 insertions(+), 68 deletions(-)
Title: Lazy (Non-Standard) Evaluation
Description: A disciplined approach to non-standard evaluation.
Author: Hadley Wickham [aut, cre],
RStudio [cph]
Maintainer: Hadley Wickham
Diff between lazyeval versions 0.1.9 dated 2014-10-01 and 0.1.10 dated 2015-01-02
DESCRIPTION | 8 ++--- MD5 | 40 +++++++++++++------------ NAMESPACE | 3 + R/as-lazy.R | 5 +++ R/names.R | 4 ++ build/vignette.rds |binary inst/doc/benchmark.html | 8 ++--- inst/doc/chained-promises.html | 6 +-- inst/doc/lazyeval.html | 64 ++++++++++++++++++++--------------------- man/all_dots.Rd | 3 + man/as.lazy.Rd | 3 + man/auto_name.Rd | 3 + man/common_env.Rd | 3 + man/interp.Rd | 3 + man/lazy_.Rd | 3 + man/lazy_dots.Rd | 3 + man/lazy_eval.Rd | 3 + man/make_call.Rd | 3 + man/missing_arg.Rd | 3 + src/lazy.c | 4 +- tests |only 21 files changed, 98 insertions(+), 74 deletions(-)
Title: Imputation of Missing Values Through a Forward Imputation
Algorithm
Description: Imputation of missing values in datasets of ordinal variables through a forward imputation algorithm
Author: Alessandro Barbiero, Pier Alda Ferrari, Giancarlo Manzi
Maintainer: Alessandro Barbiero
Diff between ForImp versions 1.0.2 dated 2013-01-31 and 1.0.3 dated 2015-01-02
ForImp-1.0.2/ForImp/doc |only ForImp-1.0.3/ForImp/DESCRIPTION | 16 ++++++++-------- ForImp-1.0.3/ForImp/MD5 | 9 ++++----- ForImp-1.0.3/ForImp/NAMESPACE | 1 + ForImp-1.0.3/ForImp/man/ForImp.Rd | 2 -- ForImp-1.0.3/ForImp/man/missingmat2.Rd | 4 ++-- 6 files changed, 15 insertions(+), 17 deletions(-)
Title: R-Based API for accessing the MSKCC Cancer Genomics Data Server
(CGDS).
Description: Provides a basic set of R functions for querying the Cancer Genomics Data Server (CGDS), hosted by the Computational Biology Center at Memorial-Sloan-Kettering Cancer Center (MSKCC).
Author: Anders Jacobsen Skanderup
Maintainer: Anders Jacobsen Skanderup
Diff between cgdsr versions 1.1.32 dated 2014-12-19 and 1.1.33 dated 2015-01-02
ChangeLog | 5 +++++ DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- R/cgdsr.R | 2 +- inst/doc/cgdsr.pdf |binary 5 files changed, 15 insertions(+), 10 deletions(-)
Title: Mixture Models for Clustering and Classification
Description: An implementation of all 14 Gaussian parsimonious
clustering models (GPCMs) for model-based clustering and
model-based classification.
Author: Ryan P. Browne, Aisha ElSherbiny and Paul D. McNicholas
Maintainer: Ryan Browne
Diff between mixture versions 1.2 dated 2014-12-27 and 1.3 dated 2015-01-02
DESCRIPTION | 6 - MD5 | 12 +- R/mixture.R | 262 +++++++++++++++++++++++++++++----------------------------- man/e.step.Rd | 2 man/gpcm.Rd | 45 ++++----- man/m.step.Rd | 7 - src/Makevars | 2 7 files changed, 167 insertions(+), 169 deletions(-)
Title: Bayesian Non- and Semi-parametric Model Fitting
Description: Markov chain Monte Carlo algorithms for non- and semi-parametric models
Author: Georgios Papageorgiou
Maintainer: Georgios Papageorgiou
Diff between BNSP versions 1.0.1 dated 2014-11-03 and 1.0.2 dated 2015-01-02
ChangeLog | 3 +++ DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- man/BNSP-package.Rd | 2 +- man/bnpglm.Rd | 2 +- 5 files changed, 13 insertions(+), 10 deletions(-)